The effect of sludge retention time (SRT) on the continuous-flow system with enhanced biological phosphorus removal (EBPR) granules at different COD loading was investigated during the operation of more than 220 days. And the results showed that when the system operated at long SRT (30 days) and low COD loading (200 mg.L-1), it could maintain excellent performance. However, long SRT and high COD loading (300 mg.L-1) deteriorated the settling ability of granules and the performance of system and resulted in the overgrowth of filamentous bacteria. Meanwhile, the transformation of poly-beta-hydroxyalkanoates (PHAs) and glycogen in metabolism process was inhibited. Moreover, the results of pyrosequencing indicated that filamentous bacteria had a competitive advantage over polyphosphate-accumulating organisms (PAOs) at high COD loading and long SRT. The PAOs specious of Candidatus_Accumlibater and system performance increased obviously when the SRT was reduced to 20 days at high COD loading. (C) 2016 Elsevier Ltd. All rights reserved.